LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-296-g061c80104a-modified)
  using 1 OpenMP thread(s) per MPI task
# Aspherical shear demo - 2d line box and triangle mixture, implicit solvent

units           lj
atom_style      line
dimension       2

read_data       data.line
Reading data file ...
  orthogonal box = (-22.553882 -22.553882 -0.5) to (22.553882 22.553882 0.5)
  2 by 2 by 1 MPI processor grid
  reading atoms ...
  350 atoms
  350 lines
  read_data CPU = 0.003 seconds

velocity        all create 1.44 320984 loop geom

neighbor        0.3 bin
neigh_modify    delay 0 every 1 check yes
neigh_modify    exclude molecule/intra all

pair_style      line/lj 2.5
pair_coeff      * * 0.25 0.25 1.0 0.25 2.5

fix             2 all rigid molecule langevin 2.0 2.0 1.0 492983
  100 rigid bodies with 350 atoms

fix             3 all deform 5 x scale 0.8 y scale 0.8
fix             4 all enforce2d

compute         10 all property/atom end1x end1y end2x end2y

#dump           1 all custom 500 dump1.atom id type x y z ix iy iz
#dump           2 all custom 500 dump1.line id type #               c_10[1] c_10[2] c_10[3] c_10[4]

timestep        0.001

compute         1 all erotate/asphere
compute         2 all ke
compute         3 all pe
variable        toteng equal (c_1+c_2+c_3)/atoms

compute_modify  thermo_temp extra/dof -350

thermo          1000
thermo_style    custom step f_2 pe ke c_1 c_2 c_3 v_toteng

run             10000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419

@Article{Gissinger24,
 author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
 title = {Type Label Framework for Bonded Force Fields in LAMMPS},
 journal = {J. Phys. Chem. B},
 year =    2024,
 volume =  128,
 number =  13,
 pages =   {3282–-3297}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 1.4, bins = 33 33 1
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair line/lj, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/2d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.736 | 4.736 | 4.736 Mbytes
   Step          f_2           PotEng         KinEng          c_1            c_2            c_3          v_toteng   
         0   1.1872976      0              0.46543528     0.03617212     0.46543528     0              0.5016074    
      1000   1.9084412     -0.001043719    0.71003395     0.089891202    0.71003395    -0.001043719    0.79888143   
      2000   2.31668       -0.020711665    0.83611544     0.13062287     0.83611544    -0.020711665    0.94602664   
      3000   2.3094506     -0.062018072    0.80584123     0.15326943     0.80584123    -0.062018072    0.8970926    
      4000   2.4383442     -0.053659995    0.86864073     0.14696993     0.86864073    -0.053659995    0.96195067   
      5000   2.5885917     -0.15612821     0.90351683     0.17156633     0.90351683    -0.15612821     0.91895494   
      6000   2.118738      -0.072041141    0.76933528     0.1155794      0.76933528    -0.072041141    0.81287354   
      7000   2.1407609     -0.057727453    0.75154404     0.13827078     0.75154404    -0.057727453    0.83208737   
      8000   2.066348      -0.097639137    0.71096217     0.14551295     0.71096217    -0.097639137    0.75883597   
      9000   2.1969096     -0.050133795    0.8028133      0.11559948     0.8028133     -0.050133795    0.86827899   
     10000   2.3932442     -0.098008752    0.83753779     0.15678193     0.83753779    -0.098008752    0.89631097   
Loop time of 0.596624 on 4 procs for 10000 steps with 350 atoms

Performance: 1448149.372 tau/day, 16760.988 timesteps/s, 5.866 Matom-step/s
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.17419    | 0.21073    | 0.27006    |   7.8 | 35.32
Neigh   | 0.0015899  | 0.0018079  | 0.0020932  |   0.5 |  0.30
Comm    | 0.041688   | 0.101      | 0.13805    |  11.3 | 16.93
Output  | 0.00011945 | 0.0001262  | 0.000143   |   0.0 |  0.02
Modify  | 0.26906    | 0.27183    | 0.27467    |   0.4 | 45.56
Other   |            | 0.01113    |            |       |  1.87

Nlocal:           87.5 ave          94 max          80 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost:           54.5 ave          67 max          42 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs:         212.75 ave         286 max         122 min
Histogram: 1 0 0 1 0 0 0 0 1 1

Total # of neighbors = 851
Ave neighs/atom = 2.4314286
Neighbor list builds = 273
Dangerous builds = 0

#undump          1
#undump          2
unfix           3

change_box      all triclinic
Changing box ...
  triclinic box = (-18.043106 -18.043106 -0.5) to (18.043106 18.043106 0.5) with tilt (0 0 0)

#dump           1 all custom 500 dump2.atom id type x y z ix iy iz
#dump           2 all custom 500 dump2.line id type #               c_10[1] c_10[2] c_10[3] c_10[4]

fix             3 all deform 1 xy erate 0.01 units box

run             10000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 1.4, bins = 26 26 1
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair line/lj, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton/tri
      stencil: half/bin/2d/tri
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.752 | 4.752 | 4.752 Mbytes
   Step          f_2           PotEng         KinEng          c_1            c_2            c_3          v_toteng   
     10000   2.3932442     -0.098029446    0.83751359     0.1568021      0.83751359    -0.098029446    0.89628624   
     11000   2.4541893     -0.15538223     0.82053681     0.19271549     0.82053681    -0.15538223     0.85787007   
     12000   2.4124449     -0.14024177     0.84559598     0.15692416     0.84559598    -0.14024177     0.86227837   
     13000   2.2095814     -0.10822636     0.73930104     0.173052       0.73930104    -0.10822636     0.80412668   
     14000   2.0946831     -0.087303541    0.77743494     0.10023865     0.77743494    -0.087303541    0.79037005   
     15000   2.0911016     -0.11524594     0.74044758     0.12978235     0.74044758    -0.11524594     0.75498398   
     16000   1.9736428     -0.17259563     0.67852978     0.13943094     0.67852978    -0.17259563     0.64536509   
     17000   2.3284367     -0.17673537     0.77018991     0.1897596      0.77018991    -0.17673537     0.78321414   
     18000   2.3178564     -0.16634746     0.81488323     0.1487365      0.81488323    -0.16634746     0.79727227   
     19000   2.7497251     -0.18254513     1.0041125      0.14528424     1.0041125     -0.18254513     0.96685165   
     20000   2.3897059     -0.12664177     0.8390411      0.15426546     0.8390411     -0.12664177     0.86666479   
Loop time of 0.79519 on 4 procs for 10000 steps with 350 atoms

Performance: 1086533.223 tau/day, 12575.616 timesteps/s, 4.401 Matom-step/s
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.26601    | 0.35051    | 0.443      |  12.3 | 44.08
Neigh   | 0.0029891  | 0.0036725  | 0.0040631  |   0.7 |  0.46
Comm    | 0.049744   | 0.14268    | 0.22734    |  19.3 | 17.94
Output  | 0.00013783 | 0.00014503 | 0.00016304 |   0.0 |  0.02
Modify  | 0.27963    | 0.28446    | 0.29049    |   0.8 | 35.77
Other   |            | 0.01372    |            |       |  1.73

Nlocal:           87.5 ave         101 max          75 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost:           61.5 ave          67 max          50 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Neighs:         244.75 ave         268 max         198 min
Histogram: 1 0 0 0 0 0 0 1 0 2

Total # of neighbors = 979
Ave neighs/atom = 2.7971429
Neighbor list builds = 289
Dangerous builds = 0
Total wall time: 0:00:01
